Hi,
I have rewritten some functions for watermark and am confinced it can upload your image, with your watermark, without any issues. To be sure I'm looking for images and watermarks that give you issues. I'll see if my code can display it well.
For example, see the image below. It's beeker (muppets) with the boonex logo (downloaded from the site and uploaded to my Dolphin site) centered.
Feel free to upload your image and watermark, I'll post the result!